HEADER HYDROLASE 13-APR-22 7ZKM TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND A TITLE 2 PSEUDO-CYCLIC THROMBIN BINDING APTAMER (TBA-NNP/DDP) - CRYSTAL FORM TITLE 3 BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: TBA-NNP/DDP; COMPND 11 CHAIN: A, B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS THROMBIN, APTAMER, COMPLEX, INHIBITOR, COAGULATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.TROISI,F.SICA REVDAT 4 31-JAN-24 7ZKM 1 JRNL REVDAT 3 14-DEC-22 7ZKM 1 JRNL REVDAT 2 07-DEC-22 7ZKM 1 JRNL REVDAT 1 30-NOV-22 7ZKM 0 JRNL AUTH R.TROISI,C.RICCARDI,K.PEREZ DE CARVASAL,M.SMIETANA,F.MORVAN, JRNL AUTH 2 P.DEL VECCHIO,D.MONTESARCHIO,F.SICA JRNL TITL A TERMINAL FUNCTIONALIZATION STRATEGY REVEALS UNUSUAL JRNL TITL 2 BINDING ABILITIES OF ANTI-THROMBIN ANTICOAGULANT APTAMERS. JRNL REF MOL THER NUCLEIC ACIDS V. 30 585 2022 JRNL REFN ESSN 2162-2531 JRNL PMID 36457701 JRNL DOI 10.1016/J.OMTN.2022.11.007 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28692 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1532 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2093 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2250 REMARK 3 NUCLEIC ACID ATOMS : 562 REMARK 3 HETEROGEN ATOMS : 259 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : -0.61000 REMARK 3 B12 (A**2) : 0.09000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.026 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3228 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4506 ; 1.531 ; 1.697 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 7.251 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;32.301 ;21.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;17.141 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.964 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 403 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2226 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 7 L 103 REMARK 3 ORIGIN FOR THE GROUP (A): -31.3183 24.3474 -23.3390 REMARK 3 T TENSOR REMARK 3 T11: 0.0332 T22: 0.2753 REMARK 3 T33: 0.3807 T12: 0.0314 REMARK 3 T13: 0.0789 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 4.2154 L22: 6.1753 REMARK 3 L33: 5.4304 L12: -0.7003 REMARK 3 L13: 0.4592 L23: -1.1279 REMARK 3 S TENSOR REMARK 3 S11: -0.2282 S12: -0.3252 S13: -0.3754 REMARK 3 S21: 0.1730 S22: 0.3046 S23: 0.9982 REMARK 3 S31: 0.1470 S32: -0.5850 S33: -0.0764 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 37 H 439 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8289 23.7664 -22.2416 REMARK 3 T TENSOR REMARK 3 T11: 0.0352 T22: 0.0321 REMARK 3 T33: 0.0347 T12: 0.0185 REMARK 3 T13: 0.0104 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 3.4202 L22: 4.0772 REMARK 3 L33: 2.2713 L12: -0.7893 REMARK 3 L13: 0.7623 L23: -0.6463 REMARK 3 S TENSOR REMARK 3 S11: -0.2046 S12: -0.1661 S13: 0.0439 REMARK 3 S21: 0.2216 S22: 0.1063 S23: -0.0128 REMARK 3 S31: 0.0270 S32: -0.0282 S33: 0.0984 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): -23.9054 25.1648 7.6331 REMARK 3 T TENSOR REMARK 3 T11: 0.6820 T22: 0.5542 REMARK 3 T33: 0.3668 T12: 0.0997 REMARK 3 T13: 0.1344 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.9108 L22: 3.8586 REMARK 3 L33: 6.7745 L12: 0.5152 REMARK 3 L13: -1.1311 L23: 2.3283 REMARK 3 S TENSOR REMARK 3 S11: -0.0785 S12: -0.3791 S13: 0.1661 REMARK 3 S21: 0.5385 S22: -0.0219 S23: -0.0763 REMARK 3 S31: -0.1892 S32: -0.3630 S33: 0.1004 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 201 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5641 10.0202 -36.6272 REMARK 3 T TENSOR REMARK 3 T11: 0.3124 T22: 0.4482 REMARK 3 T33: 0.1901 T12: 0.0895 REMARK 3 T13: 0.1036 T23: -0.0686 REMARK 3 L TENSOR REMARK 3 L11: 6.0619 L22: 6.6670 REMARK 3 L33: 2.7539 L12: 0.5467 REMARK 3 L13: -0.0759 L23: 0.0384 REMARK 3 S TENSOR REMARK 3 S11: -0.1788 S12: 0.2853 S13: 0.1593 REMARK 3 S21: -0.1952 S22: 0.0699 S23: -0.3769 REMARK 3 S31: -0.0331 S32: 0.3907 S33: 0.1089 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7ZKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292122202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30224 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 18.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 20% W/V, 2-PROPANOL 20% V/V, REMARK 280 TRISODIUM CITRATE 0.1 M, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.12667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.25333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.25333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.12667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR L -5 REMARK 465 PHE L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 GLY L -1 REMARK 465 GLU L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 THR H 146A REMARK 465 TRP H 146B REMARK 465 THR H 146C REMARK 465 ALA H 146D REMARK 465 ASN H 146E REMARK 465 VAL H 146F REMARK 465 GLY H 146G REMARK 465 LYS H 146H REMARK 465 GLY H 146I REMARK 465 DT A 7 REMARK 465 DG A 8 REMARK 465 DT A 9 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DG A 10 P OP1 OP2 REMARK 470 DT B 7 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 7 C7 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = -8.7 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 8 C3' - O3' - P ANGL. DEV. = -10.3 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 11 C3' - O3' - P ANGL. DEV. = -9.7 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE L 7 -85.67 -117.17 REMARK 500 GLU H 39 146.59 -174.64 REMARK 500 ASN H 60G 93.13 -161.68 REMARK 500 HIS H 71 -59.72 -130.70 REMARK 500 ARG H 77A 126.02 -35.92 REMARK 500 GLU H 97A -74.27 -104.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 JL0 A 101 REMARK 610 JL0 B 101 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221 O REMARK 620 2 LYS H 224 O 92.7 REMARK 620 3 HOH H 406 O 108.7 154.3 REMARK 620 4 HOH H 421 O 94.4 70.1 93.6 REMARK 620 5 HOH H 422 O 94.7 99.0 93.4 166.1 REMARK 620 6 HOH H 426 O 162.2 70.8 89.0 86.4 81.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 70.3 REMARK 620 3 DG A 5 O6 125.1 75.3 REMARK 620 4 DG A 11 O6 169.4 118.0 55.3 REMARK 620 5 DG A 14 O6 109.1 102.1 119.1 76.4 REMARK 620 6 DG A 15 O6 75.6 135.5 149.1 99.9 63.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 1 O6 REMARK 620 2 DG B 2 O6 62.9 REMARK 620 3 DG B 5 O6 119.4 68.6 REMARK 620 4 DG B 6 O6 71.4 87.0 72.0 REMARK 620 5 DG B 10 O6 115.5 160.2 98.6 74.4 REMARK 620 6 DG B 11 O6 166.9 120.1 71.8 120.6 66.5 REMARK 620 7 DG B 14 O6 94.3 74.6 105.8 160.6 124.6 75.2 REMARK 620 8 DG B 15 O6 65.0 114.3 175.6 111.1 79.5 103.8 72.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 H 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZKL RELATED DB: PDB REMARK 900 SAME PROTEIN:DNA COMPLEX IN A DIFFERENT CRYSTAL FORM REMARK 900 RELATED ID: 7ZKN RELATED DB: PDB REMARK 900 SAME PROTEIN:DNA COMPLEX IN A DIFFERENT CRYSTAL FORM REMARK 900 RELATED ID: 7ZKO RELATED DB: PDB REMARK 900 SAME PROTEIN:DNA COMPLEX IN A DIFFERENT CRYSTAL FORM DBREF 7ZKM L -5 17 UNP P00734 THRB_HUMAN 328 363 DBREF 7ZKM H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 7ZKM A 1 15 PDB 7ZKM 7ZKM 1 15 DBREF 7ZKM B 1 15 PDB 7ZKM 7ZKM 1 15 SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG SEQRES 1 B 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 B 15 DG DG HET NAG C 1 14 HET NAG C 2 14 HET 0G6 H 301 30 HET NA H 302 1 HET JL0 A 101 56 HET JKR A 102 42 HET K A 103 1 HET JL0 B 101 58 HET JKR B 102 42 HET K B 103 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM NA SODIUM ION HETNAM JL0 3-[13-METHYL-5,7,12,14-TETRAKIS(OXIDANYLIDENE)-6,13- HETNAM 2 JL0 DIAZATETRACYCLO[6.6.2.0^{4,16}.0^{11,15}]HEXADECA- HETNAM 3 JL0 1(15),2,4(16),8,10-PENTAEN-6-YL]PROPYL 3-[5,7,12,14- HETNAM 4 JL0 TETRAKIS(OXIDANYLIDENE)-13-(3-OXIDANYLPROPYL)-6,13- HETNAM 5 JL0 DIAZATETRACYCLO[6.6.2.0^{4,16}.0^{11,15}]HEXADECA-1,3, HETNAM 6 JL0 8(16),9,11(15)-PENTAEN-6-YL]PROPYL HYDROGEN PHOSPHATE HETNAM JKR 3-[5-[3-BIS(OXIDANYL)PHOSPHANYLOXYPROPOXY]NAPHTHALEN-1- HETNAM 2 JKR YL]OXYPROPYL 3-(5-OXIDANYLNAPHTHALEN-1-YL)OXYPROPYL HETNAM 3 JKR HYDROGEN PHOSPHATE HETNAM K POTASSIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN 0G6 PPACK FORMUL 5 NAG 2(C8 H15 N O6) FORMUL 6 0G6 C21 H34 CL N6 O3 1+ FORMUL 7 NA NA 1+ FORMUL 8 JL0 2(C43 H43 N4 O21 P3) FORMUL 9 JKR 2(C29 H34 O11 P2) FORMUL 10 K 2(K 1+) FORMUL 14 HOH *44(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 GLY H 246 1 13 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N GLY H 140 O GLN H 156 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.09 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.07 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.06 LINK NE2 HIS H 57 C3 0G6 H 301 1555 1555 1.50 LINK ND2 ASN H 60G C1 NAG C 1 1555 1555 1.45 LINK OG SER H 195 C2 0G6 H 301 1555 1555 1.42 LINK P DG A 1 O18 JL0 A 101 1555 1555 1.63 LINK O3' DG A 15 P1 JKR A 102 1555 1555 1.62 LINK P DG B 1 O18 JL0 B 101 1555 1555 1.60 LINK O3' DG B 15 P1 JKR B 102 1555 1555 1.64 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O ARG H 221 NA NA H 302 1555 1555 2.21 LINK O LYS H 224 NA NA H 302 1555 1555 2.38 LINK NA NA H 302 O HOH H 406 1555 1555 2.55 LINK NA NA H 302 O HOH H 421 1555 1555 2.43 LINK NA NA H 302 O HOH H 422 1555 1555 2.70 LINK NA NA H 302 O HOH H 426 1555 1555 2.59 LINK O6 DG A 1 K K A 103 1555 1555 3.05 LINK O6 DG A 2 K K A 103 1555 1555 3.00 LINK O6 DG A 5 K K A 103 1555 1555 2.81 LINK O6 DG A 11 K K A 103 1555 1555 2.88 LINK O6 DG A 14 K K A 103 1555 1555 2.83 LINK O6 DG A 15 K K A 103 1555 1555 2.83 LINK O6 DG B 1 K K B 103 1555 1555 2.85 LINK O6 DG B 2 K K B 103 1555 1555 2.98 LINK O6 DG B 5 K K B 103 1555 1555 2.86 LINK O6 DG B 6 K K B 103 1555 1555 2.86 LINK O6 DG B 10 K K B 103 1555 1555 2.80 LINK O6 DG B 11 K K B 103 1555 1555 2.87 LINK O6 DG B 14 K K B 103 1555 1555 2.69 LINK O6 DG B 15 K K B 103 1555 1555 2.76 CISPEP 1 SER H 36A PRO H 37 0 -4.84 CRYST1 76.600 76.600 129.380 90.00 90.00 120.00 P 31 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013055 0.007537 0.000000 0.00000 SCALE2 0.000000 0.015074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007729 0.00000